Well here's the question--what do you think is too big for speakers? To give you a perspective, the average bookshelf speaker is probably about 1/5 to 1/4 the size of a Antec Sonata tower case. If that's too big for your room, then you really have some limited (quality sonic) options. If you can handle the average 10"x8x8" size of a bookshelf speaker, then you're in business.
With a bookshelf you can either do nearfield (like with normal PC speakers), or a few feet back (this really lets a big sound stage build). You could have a table like the middle of the room, or even against the wall (where you are seated on the end close to the wall), and the speakers are on the other side of the room, say 5-10 feet away, depending on your room size, either hanging on the wall or on stands (or even a low shelf). There's a lot of cosmetic ways of doing this, but nearfield is always the easiest solution.
As for the amp? This really depends on your budget. You can get away with as little as $40 on a Sonic-T-amp ($20 for the T-amp, $20 for the power adaptor). It's a 10W amp essentially. Perfect for nearfield music listening, and given the high sensitivity of larger bookshelves to power input, but if you like party music, it won't be enough.
Any stereo or multichannel receiver (Onkyo TXSR501-503, any Pioneer or H&K receiver are considered good names that don't lie excessively about power output, like Sony and Yamaha tend to do). You can get these refurbed for around $100-150 online. The sweetspot receiver is Panasonic SA-XR57 right now at $300 ($220 if you can find the HDMI-less XR55, but those are harder to find). It's popular for its looks, and very clean power output, good for 200W in stereo mode, which is Class-D, unlike the more common analog amps (sometimes these are called "digital amps").
As a audio enthusiast, I'd be very happy to suggest speakers to you. There are two types I'm gonna suggest. 1) Good bang for the buck retail speakers. and 2) Very accurate internet direct speakers. In the same fashion as I did inexpensive, then more expensive amps previously.
Anyway, you can corroborate any of my listed measurements either here at soundstage av (http://www.soundstageav.com/speakermeasurements.html) or at audioholics.com.
(1) Popular retail bookshelves are Athena AS-B1/B2, and Infinity Primus 150, both can be had for around $100/pair. These are pretty accurate speakers (+/-3db accurate from a 60hz-20KHz...a comparative PC speaker system would be closer to +/- 5db from 200hz-20KHz...let's just say the bass isn't accurate enough to fit into the +/- range without expanding it horrendously).
You can find these at any Best Buy or Circuit City I believe. For a higher end offering, look for the Energy C-3, this is probably the most accurate retail speaker in its price range, which is either $250 to $500 depending on where you live, and where you find this. Good Guys might still have some of these. These guys measure pretty good, I believe almost +/- 2db from 60hz-20Khz.
(2) Internet Direct. These aren't nobodies, but guys who used to work in big retail companies, but realized there was too much bureacratic tape in order to correct probelms with the product that prevent it from being tonally accurate (or, its just to expensive because its retail).
SVS SBS-01 ($220) (www.svsound.com)
Low bass output, but very accurate, +/- 1.8db from 80-20Khz. It's sealed, meaning it won't sound boomy in a small enclosed area (like inside a bookshelf). Good for this use mostly, because you need a good sub to cover the bottom half.
AV123 X-LS ($200) (www.av123.com)
Good bass output, very accurate +/-1.75db from 60-20Khz. The accompanying sub is accurate down to 28hz (+/-3db) and only costs $200, so this is probably *the best* 2.1 system money can buy at $400, ever. Comes in a nice wood veneer. These guys made the famous Swan M200 PC loudspeakers. They company they cooborated with to make the Swans are incidentally involved with making the Infinity Primus line.
Ascend Acoustics CBM-170SE ($350) (www.ascendacoustics.com)
Err...these are my speakers. So I guess I am giving them a shoutout. Isn't as cost effective as either of the previous two, but a bit more accurate +/- 1.1db 60-20KHz. Made by a guys who used to work at the big THX speaker company M&K. It's big and black and isn't the prettiest speaker you've ever seen (just like M&K speakers), but you won't find a retail speaker that's this accurate until you are hitting the $2000s (and even then, only a few companies at that price range are this accurate...Revel in particular I'm thinking of. Of course, at $2000, you are paying $500 for the wood and craftsmanship, and probably $1000 for the name).
So, that brings me to the next point. If you go internet direct (also known as not very good looking), you can get very good performance. If you go retail, you pay for the middlemen, you pay for the brand, you pay for the advertising, and you pay for some suspicious stuff. What are these suspicious things?
If you look at high end electronics/amp/speaker companies on the retail end, a lot of the stuff they use is high quality (of course) but over the counter stuff which makes it no different than Dell vs Build it your own. The high end electronics at $2k have pretty damn good chips, but the same farroudja chips, or chroma correction, or burr brown DACs can be found in *much* cheaper online direct products. Part of this "suspicious difference" can be found in the packaging. For example, the same $30 Sonic-T amp I was suggesting to you can be bought for $150 if you want it in a nice metal case. See how expensive the box is? Now imagine those huge $1k amps. I would wager those amps aren't much different than those in a quality receiver, but the thick reinforced steel chasis may have something to do with the $1k price tag (and all the other retail related stuff). This is like any other industry. Take the LCD industry for example. There are LCDs all over the place in price, from dozens of sellers. But realistically, there are only 4 or 5 panel manufacterers. Same thing here. Alot of the stuff is the same parts, just regurgitated in a prettier package.
Just a heads up.
PS: Anyway, I personally would go with the AV123 $400 pair, and maybe pair it with a $100 H&K or Onkyo refurbed receiver off the internet. At $400, you have speakers that go way beyond most computer speakers in terms of upper harmonics, and none of the PC subs can go below 40hz anyway (we're talking about maybe -15 or more db at 40hz). This thing is FLAT to 28hz. This means you get deep in your chest bass, instead of bass that's all peaky and sounds like a one note fart. Pretty nasty. Wish I had such a sick sub =P
But if the price is too high, heading off to Best Buy and picking up a pair of Athenas isn't a bad deal either. Hell, if they are hooked up, you can listen to them there, and then walk over to the PC speaker section. Bring your own mp3 player, and play the same stuff through them. Determine for yourself if you can hear a difference; I'm not here to tell you its better or worse. It's your money, and you need to know what your priorities is. Sure beats those guys who say a $200 set of PC speakers is as good as it gets, and sounds better than any $1000 speakers don't it? Or me telling you its so worth it. All you gotta do is walk in a store, and hear for your self, rather than listen to a bunch of guys who don't know what the heck they are talking about (maybe I don't, who knows?) Such a win/win situation for *you* the buyer.